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Article

Genomic Analysis of Leptolyngbya boryana CZ1 Reveals Efficient Carbon Fixation Modules

by
Xiaohui Bai
1,*,
Honghui Wang
2,
Wenbin Cheng
3,
Junjun Wang
1,
Mengyang Ma
1,
Haihang Hu
1,
Zilong Song
1,
Hongguang Ma
1,
Yan Fan
1,4,
Chenyu Du
1 and
Jingcheng Xu
1,*
1
College of Life and Environment Science, Huangshan University, Huangshan 245041, China
2
Huangshan Institute of Product Quality Inspection, Huangshan 245000, China
3
School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
4
School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
*
Authors to whom correspondence should be addressed.
Plants 2023, 12(18), 3251; https://doi.org/10.3390/plants12183251
Submission received: 27 July 2023 / Revised: 20 August 2023 / Accepted: 11 September 2023 / Published: 13 September 2023
(This article belongs to the Special Issue Advances in Cyanobacterial Carbon Fixations and Assimilations)
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Abstract

:
Cyanobacteria, one of the most widespread photoautotrophic microorganisms on Earth, have evolved an inorganic CO2-concentrating mechanism (CCM) to adapt to a variety of habitats, especially in CO2-limited environments. Leptolyngbya boryana, a filamentous cyanobacterium, is widespread in a variety of environments and is well adapted to low-inorganic-carbon environments. However, little is currently known about the CCM of L. boryana, in particular its efficient carbon fixation module. In this study, we isolated and purified the cyanobacterium CZ1 from the Xin’anjiang River basin and identified it as L. boryana by 16S rRNA sequencing. Genome analysis revealed that L. boryana CZ1 contains β-carboxysome shell proteins and form 1B of Rubisco, which is classify it as belonging to the β-cyanobacteria. Further analysis revealed that L. boryana CZ1 employs a fine CCM involving two CO2 uptake systems NDH-13 and NDH-14, three HCO3− transporters (SbtA, BicA, and BCT1), and two carboxysomal carbonic anhydrases. Notably, we found that NDH-13 and NDH-14 are located close to each other in the L. boryana CZ1 genome and are back-to-back with the ccm operon, which is a novel gene arrangement. In addition, L. boryana CZ1 encodes two high-affinity Na+/HCO3− symporters (SbtA1 and SbtA2), three low-affinity Na+-dependent HCO3− transporters (BicA1, BicA2, and BicA3), and a BCT1; it is rare for a single strain to encode all three bicarbonate transporters in such large numbers. Interestingly, L. boryana CZ1 also uniquely encodes two active carbonic anhydrases, CcaA1 and CcaA2, which are also rare. Taken together, all these results indicated that L. boryana CZ1 is more efficient at CO2 fixation. Moreover, compared with the reported CCM gene arrangement of cyanobacteria, the CCM-related gene distribution pattern of L. boryana CZ1 was completely different, indicating a novel gene organization structure. These results can enrich our understanding of the CCM-related gene arrangement of cyanobacteria, and provide data support for the subsequent improvement and increase in biomass through cyanobacterial photosynthesis.

1. Introduction

Since the Industrial Revolution, fossil fuels have been the backbone of the world’s energy system, driving the rapid development of modern human civilization and economic growth [1,2]. However, the increasing energy demand of human activities leads to a large amount of fossil resource consumption, triggering many problems, the most important of which are energy shortages and greenhouse effects [1,3,4]. In recent years, the warming caused by the greenhouse effect has become an environmental, scientific, political, and economic issue of global concern [5]. Of all the greenhouse gases, CO2 contributes the most to the greenhouse effect [6]. The concentration of CO2 in the atmosphere increased from 0.028% before the Industrial Revolution to 0.04%, which has caused irreversible damage to the environment [7]. At present, technologies such as reducing fossil energy use, improving energy efficiency, and using new clean energy sources are mainly used to reduce CO2 production or sequestration [8]. Among these, the development of stable, safe, and environmentally acceptable carbon capture and storage technology, especially microbial carbon-sequestration technology [8,9], has become a research hotspot.
Microalgae, one of the oldest photosynthetic organisms on Earth, are typical representatives of biological carbon sequestration, which can efficiently utilize light, CO2, and water for photosynthesis to produce O2 and carbohydrates and further synthesize nutrients such as fats and proteins [10]. Microalgae can fix CO2 from the atmosphere, industrial waste gases, and soluble carbonates through photosynthesis and store chemical energy [11], and their photosynthetic efficiency is 10–50 times higher than that of plants [11,12]. In most microalgae, photosynthetic carbon metabolism is primarily based on the C3 pathway (also known as the Calvin–Benson cycle), in which the enzyme Rubisco plays an important role in the conversion of CO2 into organic compounds, but the binding of Rubisco to CO2 is very weak due to the properties of oxygenase [13,14]. At the same time, the atmospheric O2 concentration is usually higher than that of CO2, which is not conducive to carbon sequestration. In response, microalgae have evolved CCMs to increase the CO2 concentration in the vicinity of Rubisco [15]. The CCMs of microalgae include: (i) inorganic carbon uptake systems; (ii) a microcompartment containing Rubisco, such as a carboxysome [16]. Interestingly, microalgae in different habitats often have different CCM components [16,17]. Therefore, an in-depth understanding of the molecular composition and gene arrangement of CCM components in microalgae can provide us with fundamental knowledge to improve the photosynthetic efficiency of these organisms or plants.
The genus Leptolyngbya, a filamentous cyanobacteria, is widely distributed in surface soil, freshwater, brackish water, and seawater, and is well adapted to low-inorganic-carbon environments [18]. In addition, Leptolyngbya has a wide range of uses such as alloprotein production [19], biological nitrogen fixation [20], green manure and nutrient regulator for rice fields [21], and the removal of heavy metals from water bodies [22]. It is worth noting that Leptolyngbya also has a high-affinity and high-capacity CCM, which may help it to better adapt to intense white light irradiation to avoid phototoxicity, suggesting that Leptolyngbya’s CCM has novel properties [23]. However, little is known about the composition and gene distribution of Leptolyngbya’s CCM. We successfully isolated a filamentous cyanobacterium, Leptolyngbya boryana CZ1, from the Xin’anjiang River basin. Genome sequencing revealed that L. boryana CZ1 contains a β-carboxysomal shell protein and form 1B of Rubisco. An analysis of the carboxysomal shell proteins showed that L. boryana CZ1 contains all carboxysome structural proteins such as CcmK3, CcmK2, CcmK1, CcmLMN, CcmO, and CcmP, except for CcmK4. However, the structures of CcmN and CcmO were significantly different from those of the reported homologs, suggesting a novel pattern of carboxysome assembly. Further analysis revealed that L. boryana CZ1 uses a fine CCM involving two CO2 uptake systems NDH-13 and NDH-14, three HCO3− transporters, and two carbonic anhydrases. Compared with the reported CCM gene arrangement of cyanobacteria, the CCM-related gene distribution pattern of L. boryana CZ1 was completely different, indicating a novel gene organization structure. These results enrich our understanding of the CCM-related gene arrangement in cyanobacteria.

2. Results and Discussion

2.1. Isolation and Morphology of Leptolyngbya boryana CZ1

To search for algal species with a high carbon-sequestration capacity, we collected water samples from seven sampling points in the Xin’anjiang River basin every week since 2021 and isolated and purified planktonic algae from these points. The alga CZ1 was isolated from a water sample collected in November 2022. Under the optical microscope, the alga CZ1 showed slightly curved filaments, and the filaments were tightly intertwined with the colorless sheath (Figure 1A). Additionally, the filaments were composed of bright white to bright blue–green cylindrical cells separated from one to another by cross-walls.
Based on the 16S rRNA gene analysis, this algal strain is on the same evolutionary branch as Leptolyngbya boryana IU 594, L. boryana NIES-2135, L. boryana dg5, and L. boryana IAM M-101 (Figure 1B). Therefore, this algal strain was named L. boryana CZ1.

2.2. Genome Information of L. boryana CZ1

We first mapped the complete genome sequence of L. boryana CZ1. Our results showed that L. boryana CZ1 has a circular double-stranded DNA chromosome of 6,635,697 bp with a G + C content of 46.9% (Figure 2A). Prodigal V.2.6.3 [24] analyses revealed that L. boryana CZ1 has 6199 coding sequences (CDS), 3 sets of rRNA operons, and 61 tRNA genes (Table 1).
In addition, GeneMarkS v.4.28 [25] predicted that L. boryana CZ1 contains 6133 putative open reading frames (ORFs). Based on the Cluster of Orthologous Groups of proteins (COG) [26], the proteins of L. boryana CZ1 are mainly classified into energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, inorganic ion transport and metabolism, etc. Notably, approximately 1400 proteins were annotated with unknown functions (Figure 2B), suggesting that the growth and metabolism of L. boryana CZ1 are unique. antiSMASH v.7.0 [27] analyses suggested the presence of 15 gene clusters, including 5 terpenes, 3 nonribosomal peptide synthetases (NRPSs), 2 NRPS-like fragments (NRPS-likes), 3 bacteriocins, and 2 lanthipeptides. Overall, the metabolic pathway of L. boryana CZ1 needs to be further analyzed, especially the carbon-sequestration pathway.

2.3. Carboxysomes of L. boryana CZ1

Previous studies revealed that cyanobacteria depend on the CO2-concentrating mechanism (CCM) to enhance carbon-sequestration capacity and adapt to CO2 limitation in their living environments [28]. Generally, the CCM of cyanobacteria consists of two parts: carboxysomes and Ci uptake systems [16]. Therefore, we first analyzed the carboxysomes of L. boryana CZ1 based on the Prokaryotic Genome Annotation Pipeline v.6.5 (PGAP) annotation [29]. After obtaining the RbcL sequence of L. boryana CZ1, evolutionary analysis was performed with the reported RbcL sequence [30]. Our results clearly showed that the RbcL of L. boryana CZ1 belongs to Form IB (Figure 3A) according to the reported classification criteria [30]. Meanwhile, previous studies reported that β-cyanobacteria contain Form IB of Rubisco with β-carboxysomes, which encode the ccmKLMNO operon [30]. However, only the genes ccmK2, ccmK1, ccmL, and ccmM were annotated in the genome of L. boryana CZ1, and the carboxysome shell proteins CcmN, CcmO, CcmK3, CcmK4, and CcmP were missing according to the PGAP annotation (Figure 3B). The genes ccmM (gene ID Q2T42_09005) and ccmN are usually located in the same operon, so it was easy to identify the potential ccmN (gene ID Q2T42_09010), which was annotated as a hypothetical protein. Considering that the carboxysomal shell proteins CcmK and CcmO contain bacterial microcompartment (BMC) domains, we sequentially located the potential ccmK3 (gene ID Q2T42_03200), ccmP (gene ID Q2T42_04695), and ccmO (gene ID Q2T42_27155) genes. However, ccmK4 was not found.
To further confirm the above potential carboxysome shell proteins, we predicted the structures of these proteins using AlphaFold2 [31] and performed structural comparison using the Dali server [32]. A Dali search revealed that L. boryana CZ1 CcmP (gene ID Q2T42_04695) shares a similar structure with the previously reported CcmP of Synechococcus elongatus PCC7942 (PDB code: 5LT5, Z-score 36.5, sequence identity 75%) and CcmP of S. elongatus PCC 6301 (PDB code: 4HT5, Z-score 36.4, sequence identity 75%), yielding an r.m.s.d. of 0.6 and 0.5 Å over 204 and 203 Cα atoms, respectively.
Interestingly, searching with the Dali server revealed that CcmK1 (PDB code 4LIW), CcmK2 (PDB code 2A1B), and CcmK4 (PDB code 4OX6) were the structural homologs of CcmK3 (gene ID Q2T42_03200) of L. boryana CZ1, with Z-scores ranging from 16.6 to 18.8. However, multiple-sequence alignment revealed that CcmK3 of L. boryana CZ1 was significantly different from the above CcmK proteins with an extra segment of the GDKL sequence (Figure 4A). Residues involved in the formation of hexamers [33] are conserved in CcmK3 of L. boryana CZ1 (Figure 4A). In addition, BLASTp was performed to find the homolog of CcmK3 of L. boryana CZ1. Our results showed that CcmK3 of L. boryana CZ1 was conserved in Leptolyngbya sp. and was grouped into the cd07057 sequence cluster of the bacterial microcompartment (BMC) domain [34]. The evolutionary analysis of proteins in this sequence cluster showed that CcmK3 of L. boryana CZ1 was closely related to CcmK of Thermosynechococcus elongatus (Figure 4B).
Notably, we mapped ccmO (gene ID Q2T42_27155) to the ccm operon (Figure 3B). Searching with conserved domains [34] revealed that CcmO contains an N-terminal BMC domain belonging to the CcmK protein family with an unknown functional region of approximately 100 amino acids at the C-terminus (Figure 5A). Multiple-sequence alignment confirmed that the C-terminal region of L. boryana CZ1 CcmO was significantly different from CcmO of Synechocystis sp. PCC 6803 and S. elongatus PCC 7942 (Figure 5B). Subsequently, the predicted structure by AlphaFold2 showed a flexible loop region at the C-terminus of CcmO (Figure 5C). A Dali search revealed that EtuB from Clostridium kluyveri (PDB code: 3IO0, Z-score 9.7, sequence identity 20%) shares a similar structure with the N-terminal BMC domain of L. boryana CZ1 CcmO with an r.m.s.d. of 2.7 Å over 229 Cα atoms, but the loop from the C-terminus of CcmO does not match (Figure 5C). Overall, these results implied that the CcmO of L. boryana CZ1 employs a novel structure.
In addition, a homology search of CcmN (gene ID Q2T42_09010) with the Dali server revealed that S. elongatus PCC 7942 CcmN (PDB code: 7D6C, Z-score 20.3, sequence identity 50%) [35] shares a similar structure with the N-terminal domain of L. boryana CZ1 CcmN, yielding an r.m.s.d. of 0.7 Å over 121 Cα atoms. However, the C-terminus of L. boryana CZ1 CcmN contains a flexible loop region with a length of approximately 110 amino acid residues (Figure 6A). To comprehensively compare the structural differences between S. elongatus PCC 7942 CcmN and L. boryana CZ1 CcmN, we also predicted the full-length protein structure of S. elongatus PCC 7942 CcmN using AlphaFold2. The predicted structure showed that there is also a flexible loop region at the C-terminus of S. elongatus PCC 7942 CcmN, which is significantly different from L. boryana CZ1 CcmN by comparison (Figure 6B). Moreover, multiple-sequence alignment indicated that the sequence of this region in the C-terminus of CcmN is variable (Figure 6C). Overall, all these results suggested that the interaction between L. boryana CZ1 CcmN and CcmM is different from that in previous reports [17,28].
Finally, we found a second ccaA (gene ID Q2T42_07200, named ccaA2) in the L. boryana CZ1 genome, apart from the ccaA (gene ID Q2T42_17920, named ccaA1) annotated by PGAP (Figure 3B). A Dali search revealed that both L. boryana CZ1 carbonic anhydrases CcaA1 and CcaA2 share a similar structure to the previously reported CcaA of Synechocystis sp. PCC 6803 (PDB code: 5SWC). In addition, multiple-sequence alignment confirmed that residues involved in catalysis and protein–protein interactions in Synechocystis sp. PCC 6803 CcaA [36] were conserved in both L. boryana CZ1 CcaA1 and CcaA2 carbonic anhydrases, indicating that both enzymes had catalytic activity. To our knowledge, this is the first time that two active carbonic anhydrases, CcaA1 and CcaA2, have been found in the genome of cyanobacteria according to previous reports [17,28], implying that L. boryana CZ1 converts HCO3− to CO2 more efficiently.
Collectively, we located the genes encoding the shell proteins CcmK3, CcmP, CcmK2, CcmK1, CcmM, CcmN, and CcmO of the carboxysome, the CO2-fixing enzymes RbcL and RbcS, and two carbonic anhydrase CcaAs in the L. boryana CZ1 genome. However, the arrangement of these genes was different from those previously reported [17,28]. It is noteworthy that we found only CcmK3 with the absence of CcmK4 in the genome of L. boryana CZ1, suggesting a new pattern of its carboxysome assembly. In particular, for the first time to our knowledge, we identified two active carbonic anhydrases, CcaA1 and CcaA2, in the L. boryana CZ1 genome. Taken together, these results suggest that L. boryana CZ1 has adopted a novel mechanism for more efficient CO2 enrichment.

2.4. Ci Uptake Systems of L. boryana CZ1

Ci uptake systems, an important CCM, consist of three types of bicarbonate transporters and two types of CO2 uptake systems [28]. Thus, we mapped the Ci uptake systems in L. boryana CZ1. Interestingly, we easily found two types of CO2 uptake systems near the ccm operon, namely NDH-13 (encoded by cupA, ndhD3, and ndhF3) and NDH-14 (encoded by cupB, ndhD4, and ndhF4) (Figure 7A). Notably, to the best of our knowledge, this is the first report to show that NDH-13 and NDH-14 are located so close to one another in the genome compared to previous reports [17,28]. It is also noteworthy that the gene numbered Q2T42_08970, which encodes a hypothetical protein of unknown function, has an 8-base-pair overlap with cupB (Figure 7A).
In addition, the ATP-binding cassette type HCO3− transporter BCT1, encoded by cmpABCD, was found upstream of the gene ccaA2 (Figure 7A). Interestingly, a potential sbtA1 is encoded upstream of the gene cmpD, while another potential sbtA2 is removed from ccmO (Figure 7A). Searching with the Dali server revealed that both L. boryana CZ1 SbtA1 and SbtA2 share a similar structure to Synechocystis sp. PCC 6803 SbtA (PDB code: 7EGL) with an r.m.s.d. of 0.9 and 4.5 Å over 335 and 335 Cα atoms, respectively. Structural superposition showed that both L. boryana CZ1 SbtA1 and SbtA2 were well superimposed on the SbtA of Synechocystis sp. PCC 6803 (Figure 7B). Furthermore, multiple-sequence alignment revealed that residues involved in substrate binding in Synechocystis sp. PCC 6803 SbtA [37] were conserved in both L. boryana CZ1 SbtA1 and SbtA2, indicating that both transporters are functional (Figure 7C).
Finally, three potential low-affinity Na+-dependent HCO3− transporters, namely bicA1 (gene ID Q2T42_05125), bicA2 (gene ID Q2T42_06210), and bicA3 (gene ID Q2T42_19105), were located in the L. boryana CZ1 genome (Figure 7A). A structural comparison showed that the structures of the three transporters predicted by AlphaFold2 could be well superimposed onto each other (Figure 8A). Furthermore, a structural comparison using the Dali server revealed that the transmembrane domains of all three HCO3− transporters BicA1, BicA2, and BicA3 share a similar structure to the transmembrane domain of Synechocystis sp. PCC 6803 BicA (PDB code: 6KI1) (Figure 8B), but their C-terminal STAS domain [38] differed significantly (Figure 8C). Multiple-sequence alignment revealed that residues involved in substrate binding in BicA of Synechocystis sp. PCC 6803 [38] were not conserved in L. boryana CZ1 BicA1, BicA2, and BicA3 (Figure 8D), suggesting a novel feature of substrate binding.
Collectively, two types of CO2 uptake systems and three types of bicarbonate transporters have been mapped in the L. boryana CZ1 genome. Remarkably, to the best of our knowledge, we report for the first time that NDH-13 and NDH-14 are located close to each other in the genome and possibly in the same operon. Another interesting finding is that SbtA1 and BCT1 are in close proximity to each other, which is also reported for the first time compared to previous studies [17,28]. Taken together, these novel features imply that L. boryana CZ1 is able to transport CO2 and HCO3− more efficiently.

2.5. Gene Organization of the Carbon-Concentrating Mechanism in L. boryana CZ1

The distribution of CCM-related genes across the genome is crucial for the carbon-sequestration capacity of cyanobacteria. In previous studies, Klanchui et al. analyzed the distribution characteristics of CCM-related genes in 12 strains of alkaliphilic cyanobacteria [16]. Tang et al. investigated the distribution characteristics of CCM-related genes in 17 thermophilic cyanobacteria [17]. However, we found that the gene organization of CCM-related genes in L. boryana CZ1 was significantly different from that in alkaliphilic cyanobacteria and thermophilic cyanobacteria (Figure 9). The most obvious differences are as follows: (i) Ci uptake systems. All 12 alkaliphilic cyanobacteria had two CO2 uptake systems (NDH-13 and NDH-14) and BicA for HCO3− transport, while most strains lacked the high-affinity Na+/HCO3− symporter (StbA), and 8 strains lacked the HCO3− transporter BCT1 (CmpABCD) [16]. Similarly, all 17 thermophilic cyanobacteria had two CO2 uptake systems (NDH-13 and NDH-14) and BicA for HCO3− transport, while most strains lacked the high-affinity Na+/HCO3− symporter (StbA), and 4 strains lacked the HCO3− transporter BCT1 (CmpABCD) [17]. Interestingly, we found two CO2 uptake systems (NDH-13 and NDH-14), two high-affinity Na+/HCO3− symporters (sbtA1 and sbtA2), three low-affinity Na+-dependent HCO3− transporters (bicA1, bicA2, and bicA3), and one HCO3− transporter BCT1 (cmpABCD) in the L. boryana CZ1 genome (Figure 9). Notably, NDH-13 and NDH-14 were distributed in the genomes of 12 alkaliphilic cyanobacteria and 17 thermophilic cyanobacteria. In comparison, NDH-13 and NDH-14 are located close to each other in the L. boryana CZ1 genome and are found back-to-back with the ccm operon. This is a novel arrangement of genes and, as far as we know, the first time it has been discovered. Overall, these results suggest that L. boryana CZ1 is more efficient in the uptake and transport of Ci (including CO2 and HCO3−). (ii) Carboxysomal shell proteins. In total, 12 strains of alkaliphilic cyanobacteria expressed the complete β-carboxysomal shell proteins, while CcmK3/K4 was absent in only 2 strains, and only 3 strains expressed the carboxysomal β-CA, CcaA [16]. Among 17 thermophilic cyanobacteria, the β-carboxysomal shell protein CcmK2 was absent only in Thermoleptolyngbya strains, while CcmK3/K4 was absent in all Thermostichus and Thermosynechococcus strains. In addition, the carboxysomal β-CA, CcaA, was missing in all Thermostichus and Thermosynechococcus strains [17]. L. boryana CZ1 also expressed the complete set of β-carboxysomal shell proteins. However, we found that only ccmK3 is present in the L. boryana CZ1 genome, apart from the classical organization of ccmK3 and ccmK4. It is a novel discovery that ccmK3 sits alone in the genome of cyanobacteria. Sommer et al. reported that the expression of ccmK3 and ccmK4 may increase the flexibility and permeability of the carboxysome shell assembly [39], suggesting that the L. boryana CZ1 carboxysome has a different and novel assembly mode from that previously reported [16,17]. In addition, we also found two carbonic anhydrases, ccaA1 and ccaA2, which dispersed on either side of the main carboxysome locus (Figure 9). To our knowledge, we report for the first time the presence of two active carbonic anhydrases, CcaA1 and CcaA2, in the genome of cyanobacteria, indicating that L. boryana CZ1 has a more efficient HCO3− conversion capacity. Overall, the distribution characteristics of the CCM-related genes in the L. boryana CZ1 genome (Figure 9) are different from those previously reported [17,28], indicating a new gene organization and a novel mechanism of more efficient CO2 fixation. This may be the reason why Leptolyngbya has a high-affinity and high-capacity CCM, which can better adapt to intense white light irradiation to avoid phototoxicity [23].
Taken together, the distribution characteristics of CCM-related genes in the L. boryana CZ1 genome (Figure 9) were different from those previously reported [17,28], suggesting a novel gene organization and a new mechanism for more efficient CO2 fixation. This pattern of gene organization can be generalized to other L. boryana, such as L. boryana IU 594, L. boryana NIES-2135, and L. boryana dg5 (Figure 9).

3. Materials and Methods

3.1. Isolation and Identification of an Alga CZ1

To isolate carbon-sequestration bacteria, water samples were collected weekly from seven sampling sites in the Xin’anjing River basin beginning in 2021. The collected samples were transported back to the laboratory in ice bags for processing. After filtering with eight layers of gauze to remove impurities, water samples were treated with 5.0 and 1.2 µm filter membranes. The filtered membrane was repeatedly rinsed with BG11 medium, and then the elution of BG11 medium was transferred into a conical flask containing fresh BG11 medium. The conical flask was placed at 25 °C under a light intensity of 4000 lx with a 12 h light/12 h dark cycle. After 4~5 days of incubation, the grown algal solution could be used for further isolation and purification.
One milliliter of algal solution was diluted 10-fold, and then 5 µL of algal solution was placed on a slide for single algal cell isolation under an optical microscope. The picked single algal cell was transferred into a 24-well plate containing fresh BG11 medium and grown at 25 °C under a light intensity of 4000 lx with a 12 h light/12 h dark cycle. After 3 days of incubation, 5 µL of algal solution was taken for purity checking with an optical microscope. The pure algal solution was repeatedly purified on BG11 agar plates by scraping. According to the above purification methods, more than 10 strains of pure algae were obtained from the water samples of the Xin’anjiang River basin, mainly including Anabaena, Oscillatoria, and Aphanizomenon, etc. One strain of filamentous algae was named CZ1.

3.2. Genomic DNA Extraction

A single colony of CZ1 algae was selected and cultured in BG11 liquid medium to an OD680 nm of 0.6~0.8. A 200 mL algal solution of CZ1 was centrifuged at 3000 rpm at 10 °C for 10 min. The algal sediment was washed with 1× PBS buffer (10 mM Na2HPO4, 1.8 mM KH2PO4, 2.7 mM KCl, and 137 mM NaCl, pH 7.4) 2~3 times. After sufficiently grinding with liquid nitrogen, the algal sediment was resuspended in 1× lysis buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, and 1.0% SDS) and incubated at 56 °C for 1 h with 10 mg/mL proteinase K. The suspension was subsequently treated twice by adding an equal volume of chloroform–isoamyl alcohol (24:1), and the DNA was precipitated by ice-cold isopropyl alcohol. The DNA precipitate was washed twice with 75% ethanol and then resuspended in elution buffer containing 10 mM Tris pH 8.5 and 0.1 mM EDTA.

3.3. Genome Sequencing

The genome sequencing work was commissioned by Tiangen Biochemical Technology (Beijing) Co., Ltd., Beijing, China. Briefly, the sequencing library of the CZ1 genomic DNA was constructed with the ligation sequencing kit (SQK-LSK110, Oxford Nanopore Technologies, Oxford, UK) and the native barcoding expansion kit (EXP-NBD104/114, Oxford Nanopore Technologies). Genome assembly was carried out by the software Canu v.2.2 [40], and Racon v.3.3.3 [41] was used to verify the assembled qualities.

3.4. Genome Annotation and Analysis

The putative ORFs of CZ1 were annotated using Prodigal v.2.6.3 [24] and GeneMarkS v.4.28 [25]. The function of each ORF was predicted against the nonredundant protein database using the BLASTp program in NCBI (https://www.ncbi.nlm.nih.gov/, accessed on 10 April 2023). Alternatively, the assembled genome was also submitted to the GenBank database in NCBI to annotate the location and sequence of each gene and the coding proteins in the CZ1 genome using the PGAP v.6.5 [29]. The annotated genome was submitted to Proksee v1.0.0a6 [42] to draw the circular genome map. In addition, the structural proteins were predicted using AlphaFold2 [31] combined with the Dali server [32].

3.5. Phylogenetic Analysis of CZ1

The 16S rDNA of CZ1 was compared with the nr/nt nucleotide collection database in NCBI using BLASTn with the default parameters. Afterwards, the 16S rDNA sequences of 22 strains of Leptolyngbya sp. were retrieved from the hits to perform a phylogenetic analysis according to the previously reported method [43]. The 16S rDNA sequence of Escherichia coli strain U 5/41 was used as an outgroup. Multiple-sequence alignment of those sequences was constructed using the ClustalW algorithm in MEGA v.7.0.26 [44]. Subsequently, the phylogenetic tree was constructed with MEGA v.7.0.26 using the maximum-likelihood method with the default parameters and a bootstrap of 1000. Finally, iTOL v.5 [45] was used to display the phylogenetic tree.

3.6. Data Availability

The assembled genome of L. boryana CZ1 has been deposited in the GenBank database with accession number CP130144 at http://www.ncbi.nlm.nih.gov/genbank/, accessed on 10 July 2023.

4. Conclusions, Limitations, and Future Research

In this study, we isolated and identified a strain of L. boryana CZ1 from the Xin’anjiang River basin. Through whole-genome sequencing and genome analysis of L. boryana CZ1, we found that the distribution characteristics of CCM-related genes in the L. boryana CZ1 genome are different from those reported in alkaliphilic and thermophilic cyanobacteria. In particular, two CO2 uptake systems (NDH-13 and NDH-14) are located close to each other and back-to-back with the ccm operon in the L. boryana CZ1 genome, indicating a novel gene arrangement. In addition, the strain CZ1 fully encodes three bicarbonate transporters in large numbers and uniquely encodes two active carbonic anhydrases, CcaA1 and CcaA2, both of which are rare. These findings help us to better understand the diversity of CCMs in cyanobacteria and the molecular mechanism of efficient carbon sequestration. At the same time, these results are based on the L. boryana CZ1 genome analysis and protein structure prediction, which may have some limitations due to the limitations of the prior research technique. Further studies on the structure and function of the CCM-related proteins in CZ1 should be carried out using prokaryotic expression techniques, structural biology, and proteomics, etc., in order to accurately elucidate the molecular mechanism of their efficient carbon sequestration and to provide fundamental knowledge for improving the photosynthetic efficiency of these organisms or plants in the future.

Author Contributions

X.B. and J.X. designed the experiments; X.B., H.W., W.C., J.W., M.M., H.H., Z.S., H.M., Y.F., C.D. and J.X. performed the experiments; X.B., H.W., W.C. and J.X. analyzed the data; X.B., H.W. and J.X. wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Anhui Provincial Natural Science Foundation (1908085QC124), the Excellent Top-Notch Talent Project of Anhui Province (gxgwfx2020060), the Master’s degree program of Huangshan University (hsxyssd007), and the College Student’s Innovation and Entrepreneurship Training Program (202110375046, S202110375062, 202210375095, 202210375109, and 202310375022).

Data Availability Statement

Not applicable.

Acknowledgments

We thank Yong-Liang Jiang for helpful comments on our manuscript. We would like to thank Tiangen Biochemical Technology (Beijing) Co., Ltd., for the whole-genome sequencing of L. boryana CZ1.

Conflicts of Interest

The authors declare no competing financial interests.

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Figure 1. Identification of cyanobacteria CZ1. (A) Image of cyanobacteria CZ1 photographed by optical microscopy. (B) A phylogenetic tree of Leptolyngbya boryana CZ1 based on 16S rRNA sequences. The number in brackets for each strain is the accession number of the strain in the NCBI database.
Figure 1. Identification of cyanobacteria CZ1. (A) Image of cyanobacteria CZ1 photographed by optical microscopy. (B) A phylogenetic tree of Leptolyngbya boryana CZ1 based on 16S rRNA sequences. The number in brackets for each strain is the accession number of the strain in the NCBI database.
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Figure 2. Genomic characteristics of L. boryana CZ1. (A) The chromosome map of L. boryana CZ1 contains four circles. From the inside to the outside, the first circle represents the GC skew (GCskew = (G − C)/(G + C)), which measures the relative content of G and C. The second circle shows the GC content. The third circle shows the classification results of tRNA, rRNA, negative chain genes, and COG genes. The fourth circle shows the results of gene COG classification, negative chain genes, rRNA, and tRNA. (B) Schematic representation of the COG classification of L. boryana CZ1.
Figure 2. Genomic characteristics of L. boryana CZ1. (A) The chromosome map of L. boryana CZ1 contains four circles. From the inside to the outside, the first circle represents the GC skew (GCskew = (G − C)/(G + C)), which measures the relative content of G and C. The second circle shows the GC content. The third circle shows the classification results of tRNA, rRNA, negative chain genes, and COG genes. The fourth circle shows the results of gene COG classification, negative chain genes, rRNA, and tRNA. (B) Schematic representation of the COG classification of L. boryana CZ1.
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Figure 3. The carboxysome properties of L. boryana CZ1. (A) A phylogenetic tree of Form I Rubisco large subunits. The number in brackets for each protein is the accession number of the protein in the NCBI database. The corresponding branches of the higher plant Rubiscos are denoted in green. (B) Genomic structure of representative β-carboxysomal ccm operons according to a previous report [28]. Identical colors indicate that the genes have similar structural and/or functional products.
Figure 3. The carboxysome properties of L. boryana CZ1. (A) A phylogenetic tree of Form I Rubisco large subunits. The number in brackets for each protein is the accession number of the protein in the NCBI database. The corresponding branches of the higher plant Rubiscos are denoted in green. (B) Genomic structure of representative β-carboxysomal ccm operons according to a previous report [28]. Identical colors indicate that the genes have similar structural and/or functional products.
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Figure 4. Analyses of the carboxysome shell protein CcmK3 of L. boryana CZ1. (A) Multiple-sequence alignment of L. boryana CZ1 CcmK3 based on proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. (B) A phylogenetic tree of the cd07057 sequence cluster of the bacterial microcompartment (BMC) domain [34].
Figure 4. Analyses of the carboxysome shell protein CcmK3 of L. boryana CZ1. (A) Multiple-sequence alignment of L. boryana CZ1 CcmK3 based on proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. (B) A phylogenetic tree of the cd07057 sequence cluster of the bacterial microcompartment (BMC) domain [34].
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Figure 5. Analyses of the carboxysome shell protein CcmO of L. boryana CZ1. (A) Domain analysis of the carboxysome shell protein CcmO of L. boryana CZ1. (B) Multiple-sequence alignment of L. boryana CZ1 CcmO with CcmO proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. The same residues are shown in red, and those with similar properties are shown in blue. (C) Structural superposition of L. boryana CZ1 CcmO (green) on C. kluyveri EtuB (magenta, PDB code: 3IO0).
Figure 5. Analyses of the carboxysome shell protein CcmO of L. boryana CZ1. (A) Domain analysis of the carboxysome shell protein CcmO of L. boryana CZ1. (B) Multiple-sequence alignment of L. boryana CZ1 CcmO with CcmO proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. The same residues are shown in red, and those with similar properties are shown in blue. (C) Structural superposition of L. boryana CZ1 CcmO (green) on C. kluyveri EtuB (magenta, PDB code: 3IO0).
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Figure 6. Analyses of the carboxysome shell protein CcmN and carbonic anhydrases of L. boryana CZ1. (A) Structural superposition of L. boryana CZ1 CcmN (green) on S. elongatus PCC7942 CcmN (magenta, PDB code: 7D6C). (B) Structural superposition of L. boryana CZ1 CcmN (green) on S. elongatus PCC7942 CcmN (magenta, PDB code: 7D6C) and the predicted full-length protein structure of S. elongatus PCC 7942 CcmN (orange). (C) Multiple-sequence alignment of L. boryana CZ1 CcmN with CcmN proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. The same residues are shown in red, and those with similar properties are shown in blue. (D) Multiple-sequence alignment of L. boryana CZ1 CcaA1 and CcaA2 with CcaA proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. Residues involved in catalysis are labeled with triangles, and those involved in protein–protein interactions are labeled with solid dots.
Figure 6. Analyses of the carboxysome shell protein CcmN and carbonic anhydrases of L. boryana CZ1. (A) Structural superposition of L. boryana CZ1 CcmN (green) on S. elongatus PCC7942 CcmN (magenta, PDB code: 7D6C). (B) Structural superposition of L. boryana CZ1 CcmN (green) on S. elongatus PCC7942 CcmN (magenta, PDB code: 7D6C) and the predicted full-length protein structure of S. elongatus PCC 7942 CcmN (orange). (C) Multiple-sequence alignment of L. boryana CZ1 CcmN with CcmN proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. The same residues are shown in red, and those with similar properties are shown in blue. (D) Multiple-sequence alignment of L. boryana CZ1 CcaA1 and CcaA2 with CcaA proteins from Synechococcus sp. PCC 6803 and S. elongatus PCC7942. Residues involved in catalysis are labeled with triangles, and those involved in protein–protein interactions are labeled with solid dots.
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Figure 7. Properties of the Ci uptake systems of L. boryana CZ1. (A) Genomic organization of the Ci uptake systems of L. boryana CZ1. (B) Structural superimposition of L. boryana CZ1 SbtA1 (green) and SbtA2 (cyan) on Synechococcus sp. PCC 6803 SbtA (magenta, PDB code: 7EGL). (C) Multiple-sequence alignment of L. boryana CZ1 SbtA1 and SbtA2 with Synechococcus sp. PCC 6803 SbtA. Residues involved in substrate binding are labeled with triangles.
Figure 7. Properties of the Ci uptake systems of L. boryana CZ1. (A) Genomic organization of the Ci uptake systems of L. boryana CZ1. (B) Structural superimposition of L. boryana CZ1 SbtA1 (green) and SbtA2 (cyan) on Synechococcus sp. PCC 6803 SbtA (magenta, PDB code: 7EGL). (C) Multiple-sequence alignment of L. boryana CZ1 SbtA1 and SbtA2 with Synechococcus sp. PCC 6803 SbtA. Residues involved in substrate binding are labeled with triangles.
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Figure 8. Analyses of the low-affinity Na+-dependent HCO3− transporters of L. boryana CZ1. (A) Structural comparison of the low-affinity Na+-dependent HCO3− transporters BicA1, BicA2, and BicA3 from L. boryana CZ1. (B) Structural superposition of the transmembrane domain of L. boryana CZ1 BicA1 (green) on that of Synechococcus sp. PCC 6803 BicA (magenta, PDB code: 6KI1). (C) Structure comparison of the STAS domain of L. boryana CZ1 BicA1 (green) on that of Synechococcus sp. PCC 6803 BicA (magenta, PDB code: 6KI2). (D) Multiple-sequence alignment of the transmembrane domain of L. boryana CZ1 low-affinity Na+-dependent HCO3− transporters on that of Synechococcus sp. PCC 6803 BicA. Residues involved in substrate binding are labeled with triangles.
Figure 8. Analyses of the low-affinity Na+-dependent HCO3− transporters of L. boryana CZ1. (A) Structural comparison of the low-affinity Na+-dependent HCO3− transporters BicA1, BicA2, and BicA3 from L. boryana CZ1. (B) Structural superposition of the transmembrane domain of L. boryana CZ1 BicA1 (green) on that of Synechococcus sp. PCC 6803 BicA (magenta, PDB code: 6KI1). (C) Structure comparison of the STAS domain of L. boryana CZ1 BicA1 (green) on that of Synechococcus sp. PCC 6803 BicA (magenta, PDB code: 6KI2). (D) Multiple-sequence alignment of the transmembrane domain of L. boryana CZ1 low-affinity Na+-dependent HCO3− transporters on that of Synechococcus sp. PCC 6803 BicA. Residues involved in substrate binding are labeled with triangles.
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Figure 9. Genomic architecture of CCM-related genes in L. boryana CZ1. Solid arrow boxes indicate genes and transcription direction.
Figure 9. Genomic architecture of CCM-related genes in L. boryana CZ1. Solid arrow boxes indicate genes and transcription direction.
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Table 1. Genome information of L. boryana CZ1.
Table 1. Genome information of L. boryana CZ1.
FeaturesQuantitative Value
Chromosome length (bp)6,635,697
G + C content (%)46.9
Total CDS6199
Annotated CDS6133
rRNA operon3
tRNA genes61
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Bai, X.; Wang, H.; Cheng, W.; Wang, J.; Ma, M.; Hu, H.; Song, Z.; Ma, H.; Fan, Y.; Du, C.; et al. Genomic Analysis of Leptolyngbya boryana CZ1 Reveals Efficient Carbon Fixation Modules. Plants 2023, 12, 3251. https://doi.org/10.3390/plants12183251

AMA Style

Bai X, Wang H, Cheng W, Wang J, Ma M, Hu H, Song Z, Ma H, Fan Y, Du C, et al. Genomic Analysis of Leptolyngbya boryana CZ1 Reveals Efficient Carbon Fixation Modules. Plants. 2023; 12(18):3251. https://doi.org/10.3390/plants12183251

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Bai, Xiaohui, Honghui Wang, Wenbin Cheng, Junjun Wang, Mengyang Ma, Haihang Hu, Zilong Song, Hongguang Ma, Yan Fan, Chenyu Du, and et al. 2023. "Genomic Analysis of Leptolyngbya boryana CZ1 Reveals Efficient Carbon Fixation Modules" Plants 12, no. 18: 3251. https://doi.org/10.3390/plants12183251

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