Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes

The bacterial phylum Gemmatimonadetes contains members capable of performing bacteriochlorophyll-based phototrophy (chlorophototrophy). However, only one strain of chlorophototrophic Gemmatimonadetes bacteria (CGB) has been isolated to date, hampering our further understanding of their photoheterotrophic lifestyle and the evolution of phototrophy in CGB. By combining a culturomics strategy with a rapid screening technique for chlorophototrophs, we report the isolation of a new member of CGB, Gemmatimonas (G.) groenlandica sp. nov., from the surface water of a stream in the Zackenberg Valley in High Arctic Greenland. Distinct from the microaerophilic G. phototrophica strain AP64T, G. groenlandica strain TET16T is a strictly aerobic anoxygenic phototroph, lacking many oxygen-independent enzymes while possessing an expanded arsenal for coping with oxidative stresses. Its pigment composition and infra-red absorption properties are also different from G. phototrophica, indicating that it possesses a different photosystem apparatus. The complete genome sequence of G. groenlandica reveals unique and conserved features in the photosynthesis gene clusters of CGB. We further analyzed metagenome-assembled genomes of CGB obtained from soil and glacier metagenomes from Northeast Greenland, revealing a wide distribution pattern of CGB beyond the stream water investigated.

Knocking out a negative regulator of photosynthesis 1 (NRP1) increases rice leaf photosynthesis and biomass production in the field

Improving photosynthesis is a major approach to increase crop yield potential. Here we report a negative transcription factor of photosynthesis, which can be manipulated to increase rice photosynthesis and plant biomass in the field. This transcription factor named negative regulator of photosynthesis 1 (NRP1) (Os07g0471900) which was identified through a co-expression analysis using rice leaf RNA sequencing (RNA-seq) data. The NRP1 showed significantly negative correlation with the expression of many genes involved in photosynthesis. Knocking out NPR1 led to greater photosynthesis and increased biomass in the field, while overexpression of NRP1 decreased photosynthesis and biomass. Transcriptomic data analysis shows that NRP1 can negatively regulate the expression of photosynthetic genes. Protein transactivation experiments show that NRP1 is a transcription activator, implying that NRP1 may indirectly regulate photosynthesis gene expression through an unknown regulator. This study shows that combination of bioinformatics analysis with transgenic testing can be used to identify new regulators to improve photosynthetic efficiency in crops.

Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

The taxonomic status of two previously characterized Bradyrhizobium strains (58S1T and S23321) isolated from contrasting habitats in Canada and Japan was verified by genomic and phenotypic analyses. Phylogenetic analyses of five and 27 concatenated protein-encoding core gene sequences placed both strains in a highly supported lineage distinct from named species in the genus Bradyrhizobium with Bradyrhizobium betae as the closest relative. Average nucleotide identity values of genome sequences between the test and reference strains were between 84.5 and 94.2 %, which is below the threshold value for bacterial species circumscription. The complete genomes of strains 58S1T and S23321 consist of single chromosomes of 7.30 and 7.23 Mbp, respectively, and do not have symbiosis islands. The genomes of both strains have a G+C content of 64.3 mol%. Present in the genome of these strains is a photosynthesis gene cluster (PGC) containing key photosynthesis genes. A tRNA gene and its partial tandem duplication were found at the boundaries of the PGC region in both strains, which is likely the hallmark of genomic island insertion. Key nitrogen-fixation genes were detected in the genomes of both strains, but nodulation and type III secretion system genes were not found. Sequence analysis of the nitrogen fixation gene, nifH, placed 58S1T and S23321 in a novel lineage distinct from described Bradyrhizobium species. Data for phenotypic tests, including growth characteristics and carbon source utilization, supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium cosmicum sp. nov. is proposed with 58S1T (=LMG 31545T=HAMBI 3725T) as the type strain.

The Coordination and Jumps along C4 Photosynthesis Evolution in the Genus Flaveria

BackgroundC4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us to better understand the generic principles of complex trait evolution and guide engineering of C3 crops for higher yields. We used the genus Flaveria that contains C3, C3-C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis.ResultsWe mapped transcript abundance, protein sequence, and morphological features to the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features. Besides, we predicted the relative changes of ancestral nodes of those features to illustrate the key stages during the evolution of C4 photosynthesis. Gene expression and protein sequence showed consistent modification pattern along the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed, and the greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species.ConclusionsOur data shows highly coordinated changes in gene expression, protein sequence and morphological features. Besides, our results support an obviously evolutionary jump during the evolution of C4 metabolism.

Draft Genome Sequence of Aquincola tertiaricarbonis MIMtkpLc11, an Aerobic Anoxygenic Phototrophic Bacterial Strain Isolated from Biological Soil Crusts

Aquincola tertiaricarbonis strain MIMtkpLc11 was isolated from biological soil crusts in Inner Mongolia, China. The strain contains photosynthesis gene clusters.

Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans

ABSTRACTThe genusLimnohabitans(Comamonadaceae,Betaproteobacteria) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genespufLMandbchYin 28 of 46 strains from threeLimnohabitanslineages. ThepufMsequences obtained are very closely related to environmentalpufMsequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophicLimnohabitansin nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophicLimnohabitansstrains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genusLimnohabitansand also among all potentially photosyntheticBetaproteobacteriastrains. The expression of photosynthetic complexes was detected in a culture ofLimnohabitans planktonicusII-D5Tusing spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescentin situhybridization.IMPORTANCEThe data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genusLimnohabitans, indicating that they may have a novel role in freshwater habitats.

Genome-wide transcription factor binding in leaves from C3 and C4 grasses

The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3Brachypodium distachyon. In C4 species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.One sentence summaryGenome-wide patterns of transcription factor binding in vivo defined by DNaseI for leaves of C3 and C4 grasses

Arabidopsis ATHB17 coordinates nuclear and plastidic photosynthesis gene expression in response to abiotic stress

Photosynthesis is sensitive to environmental stresses. How nuclear and plastid genome coordinate to cope with abiotic stress is not well understood. Here we report that ATHB17, an Arabidopsis HD-Zip transcription factor, coordinates the expression of nuclear encoded photosynthetic genes (NEPGs) and plastid encoded genes (PEGs) in response to abiotic stress. ATHB17-overexpressing plants display enhanced stress tolerance, whereas its knockout mutant is more sensitive compared to the wild type. Through RNA-seq analysis, we found that ATHB17 down-regulated many NEPGs while up-regulated a number of PEGs. ATHB17 could directly modulate the expression of several NEPGs by binding to their promoters. Furthermore, we identified ATSIG5, encoding a plastid sigma factor, as one of the target genes of ATHB17. Loss of ATSIG5 reduced salt tolerance while overexpression of ATSIG5 enhanced salt tolerance, similar to that of ATHB17. Taken together, our results reveal that ATHB17 is an important coordinator between NEPGs and PEGs partially through ATSIG5 to protect photosynthesis machinery in response to abiotic stresses.