Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
Mol Biol Evol. 2011 Jul;28(7):2087-99. doi: 10.1093/molbev/msr032. Epub 2011 Feb 3.
Most of the major groups of eukaryotes have microbial representatives that thrive in low oxygen conditions. Those that have been studied in detail generate ATP via pathways involving anaerobically functioning enzymes of pyruvate catabolism that are typically absent in aerobic eukaryotes and whose origins remain controversial. These enzymes include pyruvate:ferredoxin oxidoreductase, pyruvate:NADP(+) oxidoreductase, and pyruvate formate lyase (Pfl). Pfl catalyzes the nonoxidative generation of formate and acetyl-Coenzyme A (CoA) from pyruvate and CoA and is activated by Pfl activating enzyme (Pfla). Within eukaryotes, this extremely oxygen-sensitive pathway was first described in the hydrogenosomes of anaerobic chytrid fungi and has more recently been characterized in the mitochondria and chloroplasts of the chlorophyte alga Chlamydomonas reinhardtii. To clarify the origins of this pathway, we have comprehensively searched for homologs of Pfl and Pfla in publicly available large-scale eukaryotic genomic and cDNA sequencing data, including our own from the anaerobic amoebozoan Mastigamoeba balamuthi. Surprisingly, we find that these enzymes are widely distributed and are present in diverse facultative or obligate anaerobic eukaryotic representatives of the archaeplastidan, metazoan, amoebozoan, and haptophyte lineages. Using maximum likelihood and Bayesian phylogenetic methods, we show that the eukaryotic Pfl and Pfla sequences each form monophyletic groups that are most closely related to homologs in firmicute gram-positive bacteria. Topology tests exclude both α-proteobacterial and cyanobacterial affinities for these genes suggesting that neither originated from the endosymbiotic ancestors of mitochondria or chloroplasts. Furthermore, the topologies of the eukaryote portion of the Pfl and Pfla trees significantly differ from well-accepted eukaryote relationships. Collectively, these results indicate that the Pfl pathway was first acquired by lateral gene transfer into a eukaryotic lineage most probably from a firmicute bacterial lineage and that it has since been spread across diverse eukaryotic groups by more recent eukaryote-to-eukaryote transfer events.
大多数真核生物的主要类群都有微生物代表，它们在低氧条件下茁壮成长。那些已经被详细研究过的微生物通过涉及无氧丙酮酸代谢的酶途径产生 ATP，这些酶通常不存在于需氧真核生物中，其起源仍然存在争议。这些酶包括丙酮酸：铁氧还蛋白氧化还原酶、丙酮酸：NADP(+)氧化还原酶和丙酮酸甲酸裂解酶（Pfl）。Pfl 催化丙酮酸和 CoA 生成甲酸和乙酰辅酶 A（CoA）的非氧化生成，并且被 Pfl 激活酶（Pfla）激活。在真核生物中，这条极其氧敏感的途径最初是在厌氧壶菌真菌的氢化体中描述的，最近在绿藻衣藻的线粒体和叶绿体中得到了描述。为了阐明这条途径的起源，我们全面搜索了 Pfl 和 Pfla 的同源物在公开的大规模真核基因组和 cDNA 测序数据中，包括我们自己从厌氧变形虫 Mastigamoeba balamuthi 中获得的数据。令人惊讶的是，我们发现这些酶广泛分布，并且存在于不同的兼性或专性厌氧真核生物代表中，包括古菌、后生动物、变形虫和甲藻门。使用最大似然法和贝叶斯系统发育方法，我们表明真核 Pfl 和 Pfla 序列各自形成单系群，与厚壁菌纲革兰阳性细菌的同源物最为密切相关。拓扑测试排除了这些基因与α-变形菌和蓝藻的亲缘关系，表明它们都不是来自线粒体或叶绿体的内共生祖先。此外，Pfl 和 Pfla 树的真核部分的拓扑结构与公认的真核生物关系有很大的不同。总的来说，这些结果表明 Pfl 途径最初是通过横向基因转移到一个真核谱系中获得的，最有可能来自厚壁菌纲细菌谱系，并且此后通过更近的真核生物到真核生物的转移事件在不同的真核生物群体中传播。
