Characteristics and functional analysis of the secondary chromosome and plasmids in sphingomonad

Song, Da; Chen, Xingjuan; Xu, Meiying

doi:10.1016/j.ibiod.2022.105402

Cited by 1 publication

(6 citation statements)

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“…According to the Blastn result against the NCBI Database, the long homologous DNA fragments of p3 with coverage ≥10% mainly existed in a few sphingomonads. Among the 109 available complete genomes of sphingomonads (including strain C1) ( 22 ), three primary chromosomes, one secondary chromosome, and 19 plasmids were found to contain the long homologous fragments. The plasmid pLA2 of Novosphingobium pentaromativorans US6-1 shared the longest homologous fragments (coverage 52%).…”

Section: Resultsmentioning

confidence: 99%

“…Second, the gene annotated as p3_rep is not a real replication initiation protein, but it regulates the replication. Although the p3_rep gene was supported by annotation with the Nr database, protein family domain search, and phylogenetic analysis ( 22 ), the highly similar proteins have not been verified experimentally. The most similar Rep protein, which has been verified, is from the plasmid pTAR of Agrobacterium tumefaciens (coverage 28.8%, identity 31.9%) ( 29 ).…”

Section: Discussionmentioning

confidence: 99%

“…In addition, there may be unknown plasmid replication initiation mechanisms. Among the 202 plasmids from sphingomonads available in the NCBI Genome Database, the rep genes were not found in 11 plasmids ( 22 ).…”

Section: Discussionmentioning

confidence: 99%

“…Compared with chromosomes, plasmids and plasmid-encoded traits are likely to evolve faster due to gene dispensability, copy number effect, horizontal gene transfer, frequent recombination, and others ( 31 , 36 ). Approximately, two-thirds of the available complete genomes of sphingomonads contain 1–11 plasmids with the low copy numbers varying from approximately 0.1 to 7.1 ( 22 ). The copy number variation, conjugational transfer, and sequence recombination of plasmids have often been observed among sphingomonads ( 22 , 37 , 38 ).…”

Section: Discussionmentioning

confidence: 99%

“…Approximately, two-thirds of the available complete genomes of sphingomonads contain 1–11 plasmids with the low copy numbers varying from approximately 0.1 to 7.1 ( 22 ). The copy number variation, conjugational transfer, and sequence recombination of plasmids have often been observed among sphingomonads ( 22 , 37 , 38 ). The long homologous DNA fragments and/or key genes of p3 and p5 were also found in some other sequenced chromosomes and plasmids of sphingomonads.…”

Section: Discussionmentioning

confidence: 99%

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The variations of native plasmids greatly affect the cell surface hydrophobicity of sphingomonads

Song,

Chen,

Yao

et al. 2023

mSystems

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The organic pollutant-degrading microorganisms with high cell surface hydrophobicity (CSH) are generally favorable due to the positive role of high CSH in pollutant capture and cell colonization. Sphingomonads, an important bacterial group with metabolic versatility, have significant potential for biodegradation and bioremediation of organic pollutants and generally harbor higher CSH than typical Gram-negative bacteria. However, the molecular mechanisms underlying their high CSH are still unclear. In this study, Sphingobium xenophagum C1, the most hydrophobic sphingomonad ever known, and its hydrophilic variant C2 were used to identify the genome variations responsible for the CSH difference by comparative genome and transcriptome analysis, as well as gene knockout verification. Our results indicated that the high CSH of strain C1 was largely attributed to the low copy number of the native plasmid p3, which mainly affected the transcriptional levels of outer membrane protein genes through direct and indirect means. In addition, loss of the genes on the native plasmid p5 involved in polysaccharide synthesis and secretion could increase CSH and cell surface friction. The bioinformatics analysis further revealed that some sphingomonad genomes also contained the long homologous fragments and/or key genes of p3 and p5. This study demonstrated the important role of native plasmids in regulating the CSH of sphingomonads, suggesting a novel CSH regulation strategy and evolution process. IMPORTANCE Microbial cell surface hydrophobicity (CSH) reflects nonspecific adhesion ability and affects various physiological processes, such as biofilm formation and pollutant biodegradation. Understanding the regulation mechanisms of CSH will contribute to illuminating microbial adaptation strategies and provide guidance for controlling CSH artificially to benefit humans. Sphingomonads, a common bacterial group with great xenobiotic-degrading ability, generally show higher CSH than typical Gram-negative bacteria, which plays a positive role in organic pollutant capture and cell colonization. This study verified that the variations of two native plasmids involved in synthesizing outer membrane proteins and polysaccharides greatly affected the CSH of sphingomonads. It is feasible to control their CSH by changing the plasmid copy number and sequences. Additionally, considering that plasmids are likely to evolve faster than chromosomes, the CSH of sphingomonads may evolve quickly to respond to environmental changes. Our results provide valuable insights into the CSH regulation and evolution of sphingomonads.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%