Department of Microbiology, 203 Morrill Science Center IVN, University of Massachusetts, 639 North Pleasant Street, Amherst, MA 01003, USA.
BMC Genomics. 2012 Sep 12;13:471. doi: 10.1186/1471-2164-13-471.
A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400 was compared to wildtype with the goal of discovering how the network for extracellular electron transfer has changed and how these two strains evolved.
Both genomes were re-annotated, resulting in 14 fewer genes (net) in the PCA genome; 28 fewer (net) in the KN400 genome; and ca. 400 gene start and stop sites moved. 96% of genes in KN400 had clear orthologs with conserved synteny in PCA. Most of the remaining genes were in regions of genomic mobility and were strain-specific or conserved in other Geobacteraceae, indicating that the changes occurred post-divergence. There were 27,270 single nucleotide polymorphisms (SNP) between the genomes. There was significant enrichment for SNP locations in non-coding or synonymous amino acid sites, indicating significant selective pressure since the divergence. 25% of orthologs had sequence differences, and this set was enriched in phosphorylation and ATP-dependent enzymes. Substantial sequence differences (at least 12 non-synonymous SNP/kb) were found in 3.6% of the orthologs, and this set was enriched in cytochromes and integral membrane proteins. Genes known to be involved in electron transport, those used in the metabolic cell model, and those that exhibit changes in expression during growth in microbial fuel cells were examined in detail.
The improvement in external electron transfer in the KN400 strain does not appear to be due to novel gene acquisition, but rather to changes in the common metabolic network. The increase in electron transfer rate and yield in KN400 may be due to changes in carbon flux towards oxidation pathways and to changes in ATP metabolism, both of which indicate that the overall energy state of the cell may be different. The electrically conductive pili appear to be unchanged, but cytochrome folding, localization, and redox potentials may all be affected, which would alter the electrical connection between the cell and the substrate.
一种新的脱硫肠状菌（Geobacter sulfurreducens）菌株 KN400 在微生物燃料电池中产生的电流比野生型 PCA 菌株更大，且还原不溶性三价铁氧化物的速度也更快。本研究旨在比较 KN400 和 PCA 的基因组，以发现细胞外电子传递网络是如何改变的，以及这两个菌株是如何进化的。
对两个基因组都进行了重新注释，结果 PCA 基因组减少了 14 个基因（净），KN400 基因组减少了 28 个基因（净），约有 400 个基因起始和终止位点发生了移动。KN400 中 96%的基因与 PCA 中有明确的直系同源物，且保守同线性。其余大部分基因位于基因组移动区域，是菌株特异性的，或在其他脱硫杆菌科中保守，这表明这些变化是在分化后发生的。两个基因组之间有 27270 个单核苷酸多态性（SNP）。SNP 位置在非编码或同义氨基酸位点有显著富集，表明自分化以来存在显著的选择压力。25%的直系同源物有序列差异，这一组富集了磷酸化和 ATP 依赖性酶。在 3.6%的直系同源物中发现了大量的序列差异（至少有 12 个非同义 SNP/kb），这一组富集了细胞色素和整合膜蛋白。对已知与电子传递有关的基因、代谢细胞模型中使用的基因以及在微生物燃料电池中生长过程中表达发生变化的基因进行了详细研究。
KN400 菌株对外电子传递的改善似乎不是由于新基因的获得，而是由于常见代谢网络的变化。KN400 中电子传递速率和产率的增加可能是由于碳通量向氧化途径的变化以及 ATP 代谢的变化，这两者都表明细胞的整体能量状态可能不同。导电菌毛似乎没有变化，但细胞色素折叠、定位和氧化还原电位可能都受到影响，这将改变细胞与底物之间的电连接。
