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When you show your results to a colleague, she suggests that your sample was contaminated with an organismfrom Earth. What approaches might you try to distinguishbetween contamination and a novel cellular life-form basedon DNA, RNA, and protein?GENERNAmt nuc mt nuc1–6It is not so difficult to imagine what it means to feedon the organic molecules that living things produce.
That is,after all, what we do. But what does it mean to “feed” on sunlight, as phototrophs do? Or, even stranger, to “feed” onrocks, as lithotrophs do? Where is the “food,” for example, inthe mixture of chemicals (H2S, H2, CO, Mn+, Fe2+, Ni2+, CH4,and NH4+) spewed forth from a hydrothermal vent?ratory gene Cox2, which encodes subunit 2 of cytochromeoxidase, was functionally transferred to the nucleus duringflowering plant evolution. Extensive analyses of plant genera have pinpointed the time of appearance of the nuclearform of the gene and identified several likely intermediates in the ultimate loss from the mitochondrial genome.A summary of Cox2 gene distributions between mitochondria and nuclei, along with data on their transcription, isshown in a phylogenetic context in Figure Q1–2.A. Assuming that transfer of the mitochondrial gene to thenucleus occurred only once (an assumption supported bythe structures of the nuclear genes), indicate the point in thephylogenetic tree where the transfer occurred.B.
Are there any examples of genera in which the transferred gene and the mitochondrial gene both appear functional? Indicate them.C. What is the minimal number of times that the mitochondrial gene has been inactivated or lost? Indicate thoseevents on the phylogenetic tree.D. What is the minimal number of times that the nucleargene has been inactivated or lost? Indicate those events onthe phylogenetic tree.E. Based on this information, propose a general schemefor transfer of mitochondrial genes to the nuclear genome.1–11 When plant hemoglobin genes were first discoveredin legumes, it was so surprising to find a gene typical of animal blood that it was hypothesized that the plant gene arose+++TephrosiaGalactiaCanavalia++++++Lespedeza++++EriosemaAtylosiaErythrina++++++RamirezellaVignaPhaseolus+++++++++Calopogonium +Pachyrhizus+++++++++++++++CologaniaPuerariaPseudeminiaPseudovigna1–8The genes for ribosomal RNA are highly conserved(relatively few sequence changes) in all organisms on Earth;thus, they have evolved very slowly over time.
Were ribosomal RNA genes “born” perfect?1–10 The process of gene transfer from the mitochondrialto the nuclear genome can be analyzed in plants. The respi-+ClitoriaDumasia1–7How many possible different trees (branching patterns) can be drawn for eubacteria, archaea, and eucaryotes,assuming that they all arose from a common ancestor?1–9Genes participating in informational processes suchas replication, transcription, and translation are transferredbetween species much less often than are genes involved inmetabolism.
The basis for this inequality is unclear at present, but one suggestion is that it relates to the underlyingcomplexity. Informational processes tend to involve largeaggregates of different gene products, whereas metabolicreactions are usually catalyzed by enzymes composed of asingle protein. Why would the complexity of the underlyingprocess—informational or metabolic—have any effect onthe rate of horizontal gene transfer?Pisum+++++OrtholobiumPsoraleaCullenGlycine++NeonotoniaTeramnusAmphicarpa++++++++++++++Figure Q1–2 Summary of Cox2 gene distribution and transcript datain a phylogenetic context (Problem 1–10).
The presence of theintact gene or a functional transcript is indicated by (+); the absenceof the intact gene or a functional transcript is indicated by (–). mt,mitochondria; nuc, nuclei.by horizontal transfer from an animal. Many morehemoglobin genes have now been sequenced, and a phylogenetic tree based on some of these sequences is shown inFigure Q1–3.A. Does this tree support or refute the hypothesis that theplant hemoglobins arose by horizontal gene transfer?B.
Supposing that the plant hemoglobin genes were originally derived from a parasitic nematode, for example, whatwould you expect the phylogenetic tree to look like?WhaleRabbit CatVERTEBRATESCobraChickenHumanSalamanderCowFrogGoldfishBarleyLotusEarthwormAlfalfaBeanInsectPLANTSClamNematodeINVERTEBRATESChlamydomonasParameciumPROTOZOAFigure Q1–3 Phylogenetic tree for hemoglobin genes from a varietyof species (Problem 1–11).
The legumes are highlighted in red.44Chapter 1: Cells and Genomes1–12 Rates of evolution appear to vary in different lineages. For example, the rate of evolution in the rat lineage issignificantly higher than in the human lineage. These ratedifferences are apparent whether one looks at changes inprotein sequences that are subject to selective pressure or atchanges in noncoding nucleotide sequences, which are notunder obvious selection pressure. Can you offer one or morepossible explanations for the slower rate of evolutionarychange in the human lineage versus the rat lineage?REFERENCESGenetic Information in EucaryotesGeneralAlberts B, Bray D, Hopkin K et al (2004) Essential Cell Biology, 2nd ed.New York: Garland Science.Barton NH, Briggs DEG, Eisen JA et al (2007) Evolution.
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